Ncbinlmnihgov typical uses of blast which bacterial

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Unformatted text preview: y” alignments •  Full perfect match (word, k ­tuple) •  Much faster than DP algorithms but less sensi1ve •  Extend alignment un1l: –  one or the other sequence ends –  score drops below a threshold Exis1ng Tools Different Sequence Alignment •  Database Search: –  BLAST, FASTA, HMMER •  Mul1ple Sequence Alignment: –  ClustalW, FSA •  Genomic Analysis: –  BLAT •  Short Read Sequence Alignment: –  BWA, BowAe, drFAST, GSNAP, SHRiMP, SOAP, MAQ BLAST •  Basic Local Alignment Search Tool •  BLAST is faster than Smith ­Waterman (DP algorithm), it cannot “guarantee the op1mal alignments of the query and database sequences”. •  A BLAST search enables a researcher to compare a query sequence with a library or database of sequences and iden1fy library sequences that resemble the query sequence above a certain threshold. •  Different types of BLASTs are available ac...
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This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

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